The Timelord Orphan
by pyromoosepoop
Summary: The eleventh doctor turns himself into a human child and makes Amy and Rory leave him at an orphanage. He's afraid a lot because of his very distant memories of death, and eventually, familiar faces from his past adopt him, and the reason he became human anyway is resurfacing so Amy and Rory come back to help the use to be Timelord and his adopted parents.
1. Chapter 1

**Disclaimer: I don't own doctor who**

 **Summary: The eleventh doctor turns himself into a human child and makes Amy and Rory leave him at an orphanage. He's afraid a lot because of his very distant memories of death, and eventually, familiar faces adopts him, and the reason he became human anyway returns**

The full moon above shed light on the tombstones. Thousands upon thousands of graves, each made of gray stone with a height of 3 inches, a length of 6 inches, and a width of 1 inch. R.I.P. they all read. I started walking forward, the stone showing where the dead lie stretch into infinity, each one the same size and shape. Now the graves are saying stuff like "wife and mother of 3" "taken away in the prime of his life" " just became a father of a newborn" etc. My walk was increasing speeds we since it started, now it was more of a sprint. "Where am I?" I asked to the never ending graves. Suddenly I ran into a black metal gate. Above it read, "Child cemetery" and under that "population 2.47 billion". On the other side, there is endless stone rectangles, varying is sizes with the biggest having a height of 1.5 inches, a length of 3 inches, and a width of half an inch, and the smallest being half the size. The biggest graves said R.I.P., the medium ones said try to R.I.P., and the smallest ones just said REST in all capital letters, as if they knew the souls of the dead youths would never rest peacefully. "WHERE AM I?" I asked nothing, my fear and sorrow for the many people put to rest bled through my voice. "you don't recognize it do you" a new voice said. I turned around to see the source of the noise, but only graves were seen. Then, out of the ground came a half decayed arm. "How typical of you" the same voice, but now full of disappointment said. I started backing away, but the metal bars of the child cemetery stopped me. A second half decade arm came from the dirt, the arms flexed as the torso made its way to the surface. The mostly decayed face looked at me with eyes filled with sorrow, regret, anger, and disappointment. "So busy running from your problems you actually forget them. You forget that YOU DID THIS!" the undead person said, anger taking over all other emotions."Please, I don't know what you're talking about or where I am. Could you please help me?" I pleaded. One decaying leg broke from the soil, and the zombie just laughed. "I can't believe you can't tell where we are since you destroyed it. How pathetic is it when you don't recognize your home." I looked around at the endless graves. Home? It can't be. "Who are you?" the other leg broke from the soil. The zombie was now completely above ground, and he laughed harder. With his brown teeth smiling he said "Rassilon. I'm Gallifrey's Lord High President. The Lord President of you and everybody you murdered. Now, Doctor, we will murder you." Rassilon raised his arms, and then the sound of soil being penetrated by decaying arms was filling the air. I started running as fast as I could. "YES! RUN DOCTOR RUN! RUN LIKE ALWAYS DO! THIS TIME, IT WONT SAVE YOU!" his laughing voice yelled. Although he wasn't moving his voice wasn't quieting. I kept running, every time I passed a grave, a decaying arm came bursting out. All around me I heard the cries of hundreds, no, THOUSANDS of voices saying "murderer" "face your fate doctor" "you're worse than every Dalek combined" "you murdered my children" "you're pure evil" and more. "STOP! PLEASE STOP" I cried… they didn't. a rock got under my shoe, at that moment, my balance deteriorated. After face planting, I looked up and found a familiar face glaring at me. "River" I half questioned, and half pleaded. "Goodbye sweetie" she said, hatred was the only emotion visible. "River please!" I cried as she put a gun to my dirt covered face. She didn't acknowledge my pleas, "and good reddens." River Song pulled the trigger.

I shot up off the floor. My heart is racing! Why am I pledged with nightmares? Why can't I remember any of them? I think my therapist, Dr. Song, was in this nightmare. Why her? Sure she diagnosed me with Panophobia, which isn't the fear of pans; it's the fear of everything. Well… I guess that includes pans… but I'm not afraid of pans though…I'm scared of stuff like cooking whisks and plungers because they kill people. Also angel statues will kill you if you look away or even blink. And robots will delete you. And drums. And tally marks tell how many things are there to kill you. And the number zero can disguise its self then kill you. And so can things covered in suctions', especially if it's red. And also plastic, and more…. Anyway, Dr. song is helping me get rid of my Panophobia so someone is more likely to adopt me. Once my fear is gone, my parents-to-be will come and admire my brilliance and how fantastic I am! My real parents will see me on the tele, as the ten year old doctor that found a cure for cancer! Sure, that's in three years, but so what? My parents are going to come and show me the combination to unlock my pocket watch, and we're going to live so happily together! I ran my fingers along the silver pocket watch on the chain around my neck and smiled. My parents are coming for me. And then they'll tell me what the weird symbol on the front means.

"Hey John, are you okay? You haven't screamed that loud in a while." A familiar voice said.

I looked at my fiend Caleb and took the cloth that mutes my nightmare-screams out of my mouth. "Ya, I'm fine. Did I wake the whole orphanage? "

"Na. Just me. The move to the attic and adding the cloth really helped with not waking any of the other kids up." Caleb said smiling. He sat down next to me, the fire from his lantern glistening off his blue eyes and ginger hair.

I looked at the flame concealed in the glass of the lantern and an image flashed across my eyes. "One time, the robots were controlling adults to obtain kids. The kids where being forced to work until the big robot was finished, and once it was, all the kids were deleted, and there was also a fire, that made an explosion." (The Next Doctor, season 4)

"Jonathan, it's just a lantern. I don't think anything will explode." The ginger nine year old replied.

"ya, you're right" I said, and looked at my pocket watch. The images of children at a military camp dying because of this watch flashed before my eyes. Of all the things I go through, I want that to stop the most.

There was a knock on my door so both Caleb and I looked at the door.

"Oh yeah, yeah, course! It's an interdimensional multi-form from outer space, they're all 'terrified' of wood!" I said, but I don't exactly know why I said it.

Caleb, being use to my random nonsense just continued looking at the door. "Come in" he said.

Ms. Olivian opened the door. She is the orphanages owners' daughter, her and her dad, Mr. Olivian, live at the orphanage. "Caleb! Jonathan! What are you two doing up? You need all the rest you can get. Don't you remember that tomorrow is the first day of 4th and 8th grade?"

"I still can't believe that even thou I'm two years older, Jonathan's grade level is twice as much as mine." Caleb said smiling at me.

I smiled back. "see ya tomorrow" I said as Caleb grabbed his lantern and joined Ms. Olivian by the door.

"Good night Jonathan" Ms. Olivian said and closed the door.

Alone again, I put the scream-muting cloth back in my mouth incase I had another nightmare. Instead, I drifted off into a dreamless sleep


	2. Chapter 2

I grabbed the suit Dr. Song gave me for my last birthday. It was a white shirt with red suspenders and a bowtie. I also grabbed the tweed jacket that she gave me on the birthday previous.

I looked at myself in the mirror and noticed a little girl behind me, she had a red balloon. Flashes of her killing people. To scared to move, I continued watching her threw the corner of my eye. I think she started saying something, but sound wasn't there. "adk dilhb" The lips read, but I wasn't that great at lip reading. "adk dilhb!" see mouthed again, she looked like she was getting louder. "DOCTOR! ADK DILHB!" She mouthed. The balloon girl looked angry, as if I was supposed to be listening. She started walking up to me, "NO! GET AWAY!" I screamed and ran out of the bathroom. I ran into the arms of my therapist, River Song. I stared at her warm smile and bright curly hair.

"It's okay" Dr. Song said as she ran her fingers threw my hair. The balloon girl was trying to say it's. Was she telling me her name? Was it a warning? "Are you ready for the first day of school?" Dr. Song asked me.

"I guess so," I replied.

"You're going to be the best eighth grader ever." Dr. Song said. We both smiled. "Before you get back to getting ready, can I see your pocket watch?" she asked. Dr. Song, for as long as I can remember, liked to hold my parents pocket watch and just stare at it, sometimes she talked to it. I handed Dr. Song my pocket watch, and she just stared at it like usual. It always looked like she was listening to something. She gave me back my watch and smiled. "You look great in that bowtie."

"Bowties are cool," I replied smiling. I fixed my bowtie.

"I'm going to finish getting ready." I told Dr. Song.

"Have fun Sweaty," She said in response. I love it when River calls me sweaty.

"Alexia Doe?" my new teacher, Mr. Ecclest, called. He was doing roll call.

Alexia was the only other orphan in Olivian Orphanage that was in eighth grade.

"Here" She said, raising her hand.

"Jonathan Doe?" He called.

Staring at Mr. Ecclest images of students being brain washed by teachers that were actually giant bats flashed across my eyes.

"Are you okay?" Alexia asked me.

"Alexia, come with me. I think the teacher is trying to brainwash us into computer slave so he can control the universe." I whisper. Looking at Alexia's face, I could tell she thought I was crazy.

"Mr. Eccest." Alexia asked raising her hand.

"Yes… Alexia, right?"

"Yes. Jonathan is here, and can me and him go and talk in the hallway for a second?"

"I don't know can you?" the bat said, likely fake smiling. He's going to kill us, I can tell.

Alexia smiled too "May we go talk in the hall way? It's a little important."

"Yes you may. Just don't disrupt other classes."

"Can do," Alexia said and looked at me, motioning he head towards the door. I follow her outside the room.

"He's plotting on killing us right now." I tell Alexia. She doesn't seem to believe me.

"John, he's not plotting murder, and he isn't trying to use us to conquer the universe."

"Then why did he bother to come to earth?" I saw more flashes of the alien bats, "And he wants me to join him."

"Jonathan, you're being insane! Not everything wants to kill you, and not everything is an alien. Trust me. There is nothing to be afraid of."

"Please, they're going to drug us through the chips and force us to do their bidding. We have to leave."

Alexia took out her phone. I know she's calling a mental asylum, or the orphanage. Why doesn't anyone call the police when I tell them that everyone's in danger?

I grabbed her arm with the phone. "Please believe me, please! I don't want any more people to die because of me! We have to go!" I could feel warm tears of fear and concern drift down my face.

"Ms. Olivian, Jonathan is freaking out. He's saying that the teacher is an alien that's trying to murder me, brain wash the whole school, and take over the universe. And he's saying he killed people again." Alexia said into the phone. "I'll stay with him until then," She likely replied.

"You don't believe me…" I mumbled looking at the floor. More tears rolled down my face.

Alexia put her hand on my shoulder. "John, you can't be scared of everything. Nobody wants to adopt a kid with hundreds of unconventional fears."

I took my watch out from under my shirt and ran my fingers across it. "And that's why I'll never get adopted. I nobody wants me, not even my parents."

"Jonathan, that's not what I meant."

"You don't have to lie Alexia." I look up at her, "I wouldn't even adopt myself. I'm the one that destroyed Gallifrey, I'm the one that killed all the Timelords, and I'm the one that will continue to mess everything up and let more humans die."

"You didn't do any of that! How could a seven year old be responsible for all that?"

Images of all the innocent Timelords I killed and their planet. That's all I could see. They're crying out for help as I watch them burn. I made them burn. I killed them. I could barely hear over the screams.

"Jonathan! Snap out of it!"

"What's going on, is he okay?"

"Mr. Eccest, he's going into one of his delusions! Help me get him out of it!"

"What is he talking about? Who did he kill?"

"Jonathan Doe, please report to the principal's office, your doctor is here to pick you up."

The screams and fire just became too loud, too hot. A young, dying Timelady comes up to me. "You're worse than a Dalek, Doctor." She started coughing. "You're the worst thing in the universe." She said as she died on my feet. I looked down at her; dead and on the ground. "It should have been you." A new Timelord said. "It should be you dead on the floor, but no. you take down a whole planet instead." I look at the dying, burning man. "You're right" I mutter. "No he's not." A new voice says. I look at this woman, with long ginger hair and a warm smile. "Doctor," She said as she wiped a tear away, "You are amazing. Don't let anything tell you otherwise, they don't know anything." The screams and flames got lowered with her every word. "But Amy-" "Doctor, think of all the people you saved. I wouldn't be alive if you didn't stop the Dalek invasion. Millions of humans wouldn't have lived if you didn't exist. Remember that." I looked at Amy, and the background started fading away, getting replaced by a room. The TARDIS control room.

Amy looked over my head. "Is that good?"

"He's snapping out of it" Rory replied.

The control room started changing to black.

"Rory," Amy said.

"He's fainting, I've got him" River said.

Blackness.

A/N: Sorry this took forever to post. Thank you so much for the reviews carlsbad, i hope you like this chapter too. Like and review if you like it.


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